"Does it matter if it (worldly accounts from the past in the bible, especially the older parts) is seen to be based on fact? Or, should one look at the message?"

Yes, it matters a lot when the stuff you're talking about is being peddled as truth. If stuff is stories provided to make a point, like Aesop's Fables, good, but don't pretend it's the truth. or try to twist it around saying that the message is the truth, etc. It isn't honest. Gospel truth and all that! I contend that Christians are discouraged from questioning the veracity of the Bible for the same reasons they're discouraged from questioning the veracity of all the other aspects of doctrine. There's a strong whiff of authoritarianism about it all.